ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/branches/development/src/nonbonded/GB.cpp
(Generate patch)

Comparing branches/development/src/nonbonded/GB.cpp (file contents):
Revision 1505 by gezelter, Sun Oct 3 22:18:59 2010 UTC vs.
Revision 1674 by gezelter, Thu Feb 16 15:59:20 2012 UTC

# Line 36 | Line 36
36   * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37   * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38   * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 < * [4]  Vardeman & Gezelter, in progress (2009).                        
39 > * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 > * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   #include <stdio.h>
# Line 222 | Line 223 | namespace OpenMD {
223          dw2 = 1.0;
224        }
225                        
226 <      GBInteractionData mixer;        
226 >      GBInteractionData mixer1, mixer2;    
227        
228        //  Cleaver paper uses sqrt of squares to get sigma0 for
229        //  mixed interactions.
230              
231 <      mixer.sigma0 = sqrt(d1*d1 + d2*d2);
232 <      mixer.xa2 = (l1*l1 - d1*d1)/(l1*l1 + d2*d2);
233 <      mixer.xai2 = (l2*l2 - d2*d2)/(l2*l2 + d1*d1);
234 <      mixer.x2 = (l1*l1 - d1*d1) * (l2*l2 - d2*d2) /
231 >      mixer1.sigma0 = sqrt(d1*d1 + d2*d2);
232 >      mixer1.xa2 = (l1*l1 - d1*d1)/(l1*l1 + d2*d2);
233 >      mixer1.xai2 = (l2*l2 - d2*d2)/(l2*l2 + d1*d1);
234 >      mixer1.x2 = (l1*l1 - d1*d1) * (l2*l2 - d2*d2) /
235          ((l2*l2 + d1*d1) * (l1*l1 + d2*d2));
236 +
237 +      mixer2.sigma0 = mixer1.sigma0;
238 +      // xa2 and xai2 for j-i pairs are reversed from the same i-j pairing.
239 +      // Swapping the particles reverses the anisotropy parameters:
240 +      mixer2.xa2 = mixer1.xai2;
241 +      mixer2.xai2 = mixer1.xa2;
242 +      mixer2.x2 = mixer1.x2;
243  
244        // assumed LB mixing rules for now:
245  
246 <      mixer.dw = 0.5 * (dw1 + dw2);
247 <      mixer.eps0 = sqrt(e1 * e2);
246 >      mixer1.dw = 0.5 * (dw1 + dw2);
247 >      mixer1.eps0 = sqrt(e1 * e2);
248 >
249 >      mixer2.dw = mixer1.dw;
250 >      mixer2.eps0 = mixer1.eps0;
251        
252        RealType er = sqrt(er1 * er2);
253 <      RealType ermu = pow(er,(1.0 / mu_));
253 >      RealType ermu = pow(er, (RealType(1.0) / mu_));
254        RealType xp = (1.0 - ermu) / (1.0 + ermu);
255        RealType ap2 = 1.0 / (1.0 + ermu);
256        
257 <      mixer.xp2 = xp * xp;
258 <      mixer.xpap2 = xp * ap2;
259 <      mixer.xpapi2 = xp / ap2;
257 >      mixer1.xp2 = xp * xp;
258 >      mixer1.xpap2 = xp * ap2;
259 >      mixer1.xpapi2 = xp / ap2;
260  
261 +      mixer2.xp2 = mixer1.xp2;
262 +      mixer2.xpap2 = mixer1.xpap2;
263 +      mixer2.xpapi2 = mixer1.xpapi2;
264 +
265        // only add this pairing if at least one of the atoms is a Gay-Berne atom
266  
267        if (atomType->isGayBerne() || atype2->isGayBerne()) {
# Line 255 | Line 270 | namespace OpenMD {
270          key1 = make_pair(atomType, atype2);
271          key2 = make_pair(atype2, atomType);
272          
273 <        MixingMap[key1] = mixer;
273 >        MixingMap[key1] = mixer1;
274          if (key2 != key1) {
275 <          MixingMap[key2] = mixer;
275 >          MixingMap[key2] = mixer2;
276          }
277        }
278      }      
279    }
280    
281 <  void GB::calcForce(InteractionData idat) {
281 >  void GB::calcForce(InteractionData &idat) {
282  
283      if (!initialized_) initialize();
284      
285 <    pair<AtomType*, AtomType*> key = make_pair(idat.atype1, idat.atype2);
271 <    GBInteractionData mixer = MixingMap[key];
285 >    GBInteractionData mixer = MixingMap[idat.atypes];
286  
287      RealType sigma0 = mixer.sigma0;
288      RealType dw     = mixer.dw;
# Line 280 | Line 294 | namespace OpenMD {
294      RealType xpap2  = mixer.xpap2;
295      RealType xpapi2 = mixer.xpapi2;
296  
297 <    Vector3d ul1 = idat.A1.getRow(2);
298 <    Vector3d ul2 = idat.A2.getRow(2);
297 >    Vector3d ul1 = idat.A1->getRow(2);
298 >    Vector3d ul2 = idat.A2->getRow(2);
299  
300      RealType a, b, g;
301  
302 <    bool i_is_LJ = idat.atype1->isLennardJones();
303 <    bool j_is_LJ = idat.atype2->isLennardJones();
304 <
302 >    bool i_is_LJ = idat.atypes.first->isLennardJones();
303 >    bool j_is_LJ = idat.atypes.second->isLennardJones();
304 >    
305      if (i_is_LJ) {
306        a = 0.0;
307        ul1 = V3Zero;
308      } else {
309 <      a = dot(idat.d, ul1);
309 >      a = dot(*(idat.d), ul1);
310      }
311  
312      if (j_is_LJ) {
313        b = 0.0;
314        ul2 = V3Zero;
315      } else {
316 <      b = dot(idat.d, ul2);
316 >      b = dot(*(idat.d), ul2);
317      }
318  
319      if (i_is_LJ || j_is_LJ)
# Line 307 | Line 321 | namespace OpenMD {
321      else
322        g = dot(ul1, ul2);
323  
324 <    RealType au = a / idat.rij;
325 <    RealType bu = b / idat.rij;
324 >    RealType au = a / *(idat.rij);
325 >    RealType bu = b / *(idat.rij);
326      
327      RealType au2 = au * au;
328      RealType bu2 = bu * bu;
# Line 321 | Line 335 | namespace OpenMD {
335      RealType e1 = 1.0 / sqrt(1.0 - x2*g2);
336      RealType e2 = 1.0 - Hp;
337      RealType eps = eps0 * pow(e1,nu_) * pow(e2,mu_);
338 <    RealType BigR = dw*sigma0 / (idat.rij - sigma + dw*sigma0);
338 >    RealType BigR = dw*sigma0 / (*(idat.rij) - sigma + dw*sigma0);
339      
340      RealType R3 = BigR*BigR*BigR;
341      RealType R6 = R3*R3;
# Line 329 | Line 343 | namespace OpenMD {
343      RealType R12 = R6*R6;
344      RealType R13 = R6*R7;
345  
346 <    RealType U = idat.vdwMult * 4.0 * eps * (R12 - R6);
346 >    RealType U = *(idat.vdwMult) * 4.0 * eps * (R12 - R6);
347  
348      RealType s3 = sigma*sigma*sigma;
349      RealType s03 = sigma0*sigma0*sigma0;
350  
351 <    RealType pref1 = - idat.vdwMult * 8.0 * eps * mu_ * (R12 - R6) / (e2 * idat.rij);
351 >    RealType pref1 = - *(idat.vdwMult) * 8.0 * eps * mu_ * (R12 - R6) /
352 >      (e2 * *(idat.rij));
353  
354 <    RealType pref2 = idat.vdwMult * 8.0 * eps * s3 * (6.0*R13 - 3.0*R7) /(dw*idat.rij*s03);
354 >    RealType pref2 = *(idat.vdwMult) * 8.0 * eps * s3 * (6.0*R13 - 3.0*R7) /
355 >      (dw*  *(idat.rij) * s03);
356  
357 <    RealType dUdr = - (pref1 * Hp + pref2 * (sigma0*sigma0*idat.rij/s3 + H));
357 >    RealType dUdr = - (pref1 * Hp + pref2 * (sigma0 * sigma0 *  
358 >                                             *(idat.rij) / s3 + H));
359      
360      RealType dUda = pref1 * (xpap2*au - xp2*bu*g) / (1.0 - xp2 * g2)
361        + pref2 * (xa2 * au - x2 *bu*g) / (1.0 - x2 * g2);
# Line 350 | Line 367 | namespace OpenMD {
367        + 8.0 * eps * mu_ * (R12 - R6) * (xp2*au*bu - Hp*xp2*g) /
368        (1.0 - xp2 * g2) / e2 + 8.0 * eps * s3 * (3.0 * R7 - 6.0 * R13) *
369        (x2 * au * bu - H * x2 * g) / (1.0 - x2 * g2) / (dw * s03);
353 –    
370  
371 <    Vector3d rhat = idat.d / idat.rij;  
372 <    Vector3d rxu1 = cross(idat.d, ul1);
373 <    Vector3d rxu2 = cross(idat.d, ul2);
371 >    Vector3d rhat = *(idat.d) / *(idat.rij);  
372 >    Vector3d rxu1 = cross(*(idat.d), ul1);
373 >    Vector3d rxu2 = cross(*(idat.d), ul2);
374      Vector3d uxu = cross(ul1, ul2);
359 –    
360 –    idat.pot += U*idat.sw;
361 –    idat.f1 += dUdr * rhat + dUda * ul1 + dUdb * ul2;    
362 –    idat.t1 += dUda * rxu1 - dUdg * uxu;
363 –    idat.t2 += dUdb * rxu2 - dUdg * uxu;
364 –    idat.vpair += U*idat.sw;
375  
376 +    (*(idat.pot))[VANDERWAALS_FAMILY] += U *  *(idat.sw);
377 +    *(idat.f1) += dUdr * rhat + dUda * ul1 + dUdb * ul2;    
378 +    *(idat.t1) += dUda * rxu1 - dUdg * uxu;
379 +    *(idat.t2) += dUdb * rxu2 + dUdg * uxu;
380 +    *(idat.vpair) += U * *(idat.sw);
381 +
382      return;
383  
384    }
385  
386 <  RealType GB::getSuggestedCutoffRadius(AtomType* at1, AtomType* at2) {
386 >  RealType GB::getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes) {
387      if (!initialized_) initialize();  
388  
389      RealType cut = 0.0;
390  
391 <    if (at1->isGayBerne()) {
392 <      GayBerneParam gb1 = getGayBerneParam(at1);
391 >    if (atypes.first->isGayBerne()) {
392 >      GayBerneParam gb1 = getGayBerneParam(atypes.first);
393        RealType d1 = gb1.GB_d;
394        RealType l1 = gb1.GB_l;
395        // sigma is actually sqrt(2)*l  for prolate ellipsoids
396 <      cut = max(cut, 2.5 * sqrt(2.0) * max(d1, l1));
397 <    } else if (at1->isLennardJones()) {
398 <      cut = max(cut, 2.5 * getLJSigma(at1));
396 >      cut = max(cut, RealType(2.5) * sqrt(RealType(2.0)) * max(d1, l1));
397 >    } else if (atypes.first->isLennardJones()) {
398 >      cut = max(cut, RealType(2.5) * getLJSigma(atypes.first));
399      }
400  
401 <    if (at2->isGayBerne()) {
402 <      GayBerneParam gb2 = getGayBerneParam(at2);
401 >    if (atypes.second->isGayBerne()) {
402 >      GayBerneParam gb2 = getGayBerneParam(atypes.second);
403        RealType d2 = gb2.GB_d;
404        RealType l2 = gb2.GB_l;
405 <      cut = max(cut, 2.5 * sqrt(2.0) * max(d2, l2));
406 <    } else if (at1->isLennardJones()) {
407 <      cut = max(cut, 2.5 * getLJSigma(at2));
405 >      cut = max(cut, RealType(2.5) * sqrt(RealType(2.0)) * max(d2, l2));
406 >    } else if (atypes.second->isLennardJones()) {
407 >      cut = max(cut, RealType(2.5) * getLJSigma(atypes.second));
408      }
409    
410      return cut;

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines